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Fix communication bug of ILP

This commit is contained in:
oywg11 2019-08-01 16:38:19 +03:00
parent d09ca91627
commit 8f5cd8661f
26 changed files with 5194 additions and 1516 deletions
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doc/src/Eqs/pair_kolmogorov_crespi_full.jpg
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doc/src/Eqs/pair_kolmogorov_crespi_full.tex
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@ -27,7 +27,7 @@
V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
\rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
\rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\[15pt]
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
\end{eqnarray*}
\endgroup
\end{document}

2
doc/src/pair_coul_shield.txt
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@ -13,7 +13,7 @@ pair_style coul/shield command :h3
pair_style coul/shield cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]

28
doc/src/pair_ilp_graphene_hbn.txt
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@ -13,17 +13,17 @@ pair_style ilp/graphene/hbn command :h3
pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]
pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
pair_coeff * * ilp/graphene/hbn ../potentials/BNCH.ILP B N C :pre
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
pair_coeff * * rebo CH.rebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C
pair_coeff * * rebo ../potentials/CH.rebo NULL NULL C
pair_coeff * * tersoff ../potentials/BNC.tersoff B N NULL
pair_coeff * * ilp/graphene/hbn ../potentials/BNCH.ILP B N C
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.695
pair_coeff 2 2 coul/shield 0.69 :pre
@ -85,6 +85,22 @@ be found in "(Ouyang)"_#Ouyang.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
{E_vdW} = vdW (attractive) energy
{E_Rep} = Repulsive energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute 0 all pair ilp/graphene/hbn
variable Evdw equal c_0\[1\]
variable Erep equal c_0\[2\]
thermo_style custom step temp epair v_Erep v_Evdw :pre
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:

24
doc/src/pair_kolmogorov_crespi_full.txt
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@ -13,17 +13,17 @@ pair_style kolmogorov/crespi/full command :h3
pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
tap_flag = 0/1 to turn off/on the taper function :ul
[Examples:]
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CH.KC C C :pre
pair_coeff * * kolmogorov/crespi/full ../potentials/CH.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
pair_coeff * * rebo CH.rebo C H
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H :pre
pair_coeff * * rebo ../potentials/CH.rebo C H
pair_coeff * * kolmogorov/crespi/full ../potentials/CH_taper.KC C H :pre
[Description:]
@ -74,6 +74,22 @@ comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 2.
The 2 values correspond to the following sub-categories:
{E_vdW} = vdW (attractive) energy
{E_Rep} = Repulsive energy :ol
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
compute 0 all pair kolmogorov/crespi/full
variable Evdw equal c_0\[1\]
variable Erep equal c_0\[2\]
thermo_style custom step temp epair v_Erep v_Evdw :pre
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:

1
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH.ILP Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/BNCH.ILP

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examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/Bi_gr_AB_stack_2L_noH.data Normal file
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examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.rebo Symbolic link
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../../../../../potentials/CH.rebo

49
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene
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@ -5,21 +5,22 @@ atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
read_data Bi_gr_AB_stack_2L_noH.data
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
group adsorbate type 2
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP C C # long range
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
@ -27,35 +28,25 @@ neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0
variable ILP equal c_1
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
fix thermostat all nve
run 1000

128
examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.1 Normal file
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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 molecule ids so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.00018123 secs
read_data CPU = 0.00179349 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 20.52 | 20.52 | 20.52 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
0 0.0000000000000000 -10037.2853168513975106 -10089.9846779678973689 52.6993611164999436 -10057.1894932863488066 -32.7951846815484842 43.6401037466550932 -76.4352884281863538 299.9999999999996589
100 5.4714687280356884 -10037.0338552868142870 -10064.7651651140276954 27.7313098272134866 -10032.1809546658514591 -32.5842104481769326 34.7308676709731401 -67.3150781191208409 157.8651576016785896
200 10.9391297820257023 -10036.9626863095945737 -10061.1437965401473775 24.1811102305520329 -10028.8556641958457476 -32.2881323443021699 28.1799358234288526 -60.4680681676962450 137.6550477173489071
300 16.5882020250428468 -10037.0034097789539373 -10063.5001355365984637 26.4967257576440751 -10030.8230306457862753 -32.6771048908121244 34.9238490632189666 -67.6009539540019659 150.8370795942042264
400 22.1194989730138332 -10037.0320901258455706 -10064.3886163746337843 27.3565262487876240 -10031.8532011416427849 -32.5354152329904451 44.2423469839209460 -76.7777622168925546 155.7316388806602561
500 27.6722563949879259 -10037.0233394483148004 -10064.1136184894730832 27.0902790411580163 -10031.4312007416901906 -32.6824177477829565 37.2292320482101289 -69.9116497959676906 154.2159817531989177
600 33.2032995349727571 -10037.0033561502987141 -10063.6570740290953836 26.6537178787960869 -10031.3274097829344100 -32.3296642461602843 28.5090732059975061 -60.8387374521216842 151.7307837178934449
700 38.6685221369843930 -10037.0041655805853225 -10063.3498627390818001 26.3456971584966979 -10030.8006321783104795 -32.5492305607709014 32.5646861904578486 -65.1139167511948074 149.9773238251721921
800 44.2185375869739801 -10037.0245724491269357 -10064.2193369538654224 27.1947645047377584 -10031.7656842933574808 -32.4536526605085243 43.3815569718683705 -75.8352096323569498 154.8107828743098082
900 49.6989215560024604 -10037.0283918584391358 -10064.6675188165245345 27.6391269580851500 -10032.1673975747289660 -32.5001212417962648 39.9934500237055133 -72.4935712654787778 157.3403910741040761
1000 55.1455117090372369 -10037.0033475406326033 -10063.6621727186211501 26.6588251779885006 -10031.3371200905367004 -32.3250526280852100 29.5735783776502288 -61.8986310057011480 151.7598578798047697
Loop time of 55.1456 on 1 procs for 1000 steps with 1360 atoms
Performance: 1.567 ns/day, 15.318 hours/ns, 18.134 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 55.092 | 55.092 | 55.092 | 0.0 | 99.90
Bond | 0.00050265 | 0.00050265 | 0.00050265 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.032649 | 0.032649 | 0.032649 | 0.0 | 0.06
Output | 0.00060948 | 0.00060948 | 0.00060948 | 0.0 | 0.00
Modify | 0.0093351 | 0.0093351 | 0.0093351 | 0.0 | 0.02
Other | | 0.01008 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:55

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examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.5Jun19.bilayer-graphene.icc.4 Normal file
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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 molecule ids so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000147377 secs
read_data CPU = 0.0025185 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
0 0.0000000000000000 -10037.2853168516194273 -10089.9846779681192857 52.6993611164999933 -10057.1894932866325689 -32.7951846814872354 43.6401037466782640 -76.4352884281594527 299.9999999999999432
100 1.5180878639221191 -10037.0338552867851831 -10064.7651651139967726 27.7313098272123320 -10032.1809546658569161 -32.5842104481406381 34.7308676709827395 -67.3150781191209546 157.8651576016720242
200 3.0293023219564930 -10036.9626863095381850 -10061.1437965400909889 24.1811102305529495 -10028.8556641958311957 -32.2881323442601911 28.1799358234373614 -60.4680681676959750 137.6550477173541367
300 4.5289151089964435 -10037.0034097789121006 -10063.5001355365566269 26.4967257576439188 -10030.8230306457808183 -32.6771048907772084 34.9238490632284311 -67.6009539540031454 150.8370795942033453
400 6.0309539699228480 -10037.0320901258182857 -10064.3886163746046805 27.3565262487870413 -10031.8532011416427849 -32.5354152329611424 44.2423469839354624 -76.7777622168941747 155.7316388806569307
500 7.5873900629812852 -10037.0233394482729636 -10064.1136184894312464 27.0902790411581904 -10031.4312007416810957 -32.6824177477510176 37.2292320482201404 -69.9116497959683159 154.2159817531999124
600 9.1088078819448128 -10037.0033561502586963 -10063.6570740290553658 26.6537178787959803 -10031.3274097829398670 -32.3296642461160033 28.5090732060055281 -60.8387374521202773 151.7307837178928480
700 10.6168858460150659 -10037.0041655805125629 -10063.3498627390090405 26.3456971584962574 -10030.8006321782777377 -32.5492305607314165 32.5646861904650535 -65.1139167511946653 149.9773238251696910
800 12.1294107990106568 -10037.0245724491123838 -10064.2193369538508705 27.1947645047383304 -10031.7656842933720327 -32.4536526604775162 43.3815569718824179 -75.8352096323571629 154.8107828743130767
900 13.6509861790109426 -10037.0283918584264029 -10064.6675188165099826 27.6391269580827625 -10032.1673975747471559 -32.5001212417642336 39.9934500237184380 -72.4935712654798436 157.3403910740904905
1000 15.1634582940023392 -10037.0033475405834906 -10063.6621727185720374 26.6588251779879926 -10031.3371200905276055 -32.3250526280445740 29.5735783776581442 -61.8986310057012972 151.7598578798018707
Loop time of 15.1635 on 4 procs for 1000 steps with 1360 atoms
Performance: 5.698 ns/day, 4.212 hours/ns, 65.948 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.997 | 14.363 | 14.741 | 9.0 | 94.72
Bond | 0.00036359 | 0.00040186 | 0.00044586 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.40664 | 0.78485 | 1.1509 | 38.6 | 5.18
Output | 0.00027687 | 0.00036825 | 0.00063194 | 0.0 | 0.00
Modify | 0.0043962 | 0.0045847 | 0.0047857 | 0.2 | 0.03
Other | | 0.01055 | | | 0.07
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4628 ave 4628 max 4628 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259250 ave 259250 max 259250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

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examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNC.tersoff Symbolic link
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../../../../../potentials/BNC.tersoff

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examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/BNCH.ILP Symbolic link
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../../../../../potentials/BNCH.ILP

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examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/hBN_AA_prime_stack_2L_noH.data Normal file
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examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/in.bilayer-hBN Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost error
###### Run molecular dynamics ######
run 1000

144
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@ -0,0 +1,144 @@
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000162885 secs
read_data CPU = 0.00152144 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost error
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 39.16 | 39.16 | 39.16 Mbytes
Step CPU TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
0 0.0000000000 -10193.1380848266 -10245.8374459431 52.6993611165 -77.5570687695 -10208.7302118650 -36.7764829084 40.7805858612 -77.5570687695 -0.3307511697 300.0000000000
100 6.7965245070 -10192.8138221665 -10215.1933919318 22.3795697653 -80.9976194405 -10177.8775571602 -36.9677356248 44.0298838157 -80.9976194405 -0.3480991468 127.3994748197
200 13.6121753111 -10192.9217984546 -10221.8066529747 28.8848545200 -86.3703194681 -10184.2512197444 -37.1689855905 49.2013338776 -86.3703194681 -0.3864476398 164.4319052911
300 20.4697002331 -10192.8780091121 -10219.0294731325 26.1514640204 -83.0639240055 -10182.3487520151 -36.3041195435 46.7598044620 -83.0639240055 -0.3766015739 148.8716189324
400 27.2477328760 -10192.8915023008 -10218.8337311224 25.9422288216 -78.3942416895 -10181.3978178066 -37.1109676261 41.2832740634 -78.3942416895 -0.3249456897 147.6805122794
500 34.0398510781 -10192.9091924320 -10221.3314056924 28.4222132604 -81.7685306349 -10184.0302799036 -36.9462261394 44.8223044955 -81.7685306349 -0.3548996493 161.7982419039
600 40.8147194131 -10192.8859685989 -10219.3709182378 26.4849496389 -86.2783346104 -10182.6694059460 -36.2951497597 49.9831848507 -86.2783346104 -0.4063625321 150.7700420526
700 47.6096971680 -10192.9015812429 -10220.9496893393 28.0481080963 -82.2887300963 -10183.2081700333 -37.3937397296 44.8949903667 -82.2887300963 -0.3477795764 159.6685851711
800 54.4165411390 -10192.8798040842 -10218.5099898620 25.6301857778 -78.0110194568 -10181.4267315419 -36.7542088970 41.2568105599 -78.0110194568 -0.3290494232 145.9041546318
900 61.2580328170 -10192.8940657565 -10220.5595028458 27.6654370893 -82.4743793723 -10183.8013123118 -36.3811572492 46.0932221231 -82.4743793723 -0.3770332848 157.4901659330
1000 68.0452993071 -10192.8973362869 -10219.0104657947 26.1131295079 -87.1256831340 -10181.2524878789 -37.3618984004 49.7637847337 -87.1256831340 -0.3960795154 148.6533932553
Loop time of 68.0453 on 1 procs for 1000 steps with 1360 atoms
Performance: 1.270 ns/day, 18.901 hours/ns, 14.696 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 67.995 | 67.995 | 67.995 | 0.0 | 99.93
Bond | 0.00047219 | 0.00047219 | 0.00047219 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.030427 | 0.030427 | 0.030427 | 0.0 | 0.04
Output | 0.000568 | 0.000568 | 0.000568 | 0.0 | 0.00
Modify | 0.0089312 | 0.0089312 | 0.0089312 | 0.0 | 0.01
Other | | 0.01005 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7836 ave 7836 max 7836 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249560 ave 249560 max 249560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1005040
Ave neighs/atom = 739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:08

144
examples/USER/misc/ilp_graphene_hbn/bilayer-hBN/log.5Jun19.bilayer_hBN.icc.4 Normal file
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@ -0,0 +1,144 @@
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.00013403 secs
read_data CPU = 0.00236647 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step cpu etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost error
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 20.72 | 20.72 | 20.72 Mbytes
Step CPU TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
0 0.0000000000 -10193.1380848270 -10245.8374459435 52.6993611165 -77.5570687695 -10208.7302118654 -36.7764829083 40.7805858612 -77.5570687695 -0.3307511697 300.0000000000
100 2.1550989150 -10192.8138221665 -10215.1933919317 22.3795697653 -80.9976194405 -10177.8775571601 -36.9677356248 44.0298838158 -80.9976194405 -0.3480991468 127.3994748197
200 4.3479236889 -10192.9217984546 -10221.8066529746 28.8848545200 -86.3703194681 -10184.2512197444 -37.1689855904 49.2013338777 -86.3703194681 -0.3864476398 164.4319052911
300 6.5410459590 -10192.8780091121 -10219.0294731324 26.1514640204 -83.0639240055 -10182.3487520151 -36.3041195435 46.7598044620 -83.0639240055 -0.3766015739 148.8716189324
400 8.7036962360 -10192.8915023008 -10218.8337311224 25.9422288216 -78.3942416895 -10181.3978178066 -37.1109676261 41.2832740634 -78.3942416895 -0.3249456897 147.6805122794
500 10.8535934120 -10192.9091924320 -10221.3314056923 28.4222132604 -81.7685306349 -10184.0302799036 -36.9462261394 44.8223044955 -81.7685306349 -0.3548996493 161.7982419039
600 12.9922130840 -10192.8859685988 -10219.3709182377 26.4849496389 -86.2783346104 -10182.6694059459 -36.2951497597 49.9831848507 -86.2783346104 -0.4063625321 150.7700420526
700 15.1486390879 -10192.9015812430 -10220.9496893393 28.0481080963 -82.2887300963 -10183.2081700333 -37.3937397295 44.8949903668 -82.2887300963 -0.3477795764 159.6685851711
800 17.3069961029 -10192.8798040842 -10218.5099898620 25.6301857778 -78.0110194568 -10181.4267315419 -36.7542088969 41.2568105599 -78.0110194568 -0.3290494232 145.9041546318
900 19.4832645269 -10192.8940657564 -10220.5595028457 27.6654370893 -82.4743793723 -10183.8013123118 -36.3811572492 46.0932221231 -82.4743793723 -0.3770332848 157.4901659330
1000 21.6507079899 -10192.8973362868 -10219.0104657947 26.1131295079 -87.1256831340 -10181.2524878789 -37.3618984003 49.7637847337 -87.1256831340 -0.3960795154 148.6533932553
Loop time of 21.6507 on 4 procs for 1000 steps with 1360 atoms
Performance: 3.991 ns/day, 6.014 hours/ns, 46.188 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.152 | 20.681 | 21.202 | 8.2 | 95.52
Bond | 0.00039643 | 0.00043971 | 0.00048381 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.43171 | 0.9526 | 1.482 | 38.2 | 4.40
Output | 0.00028839 | 0.00037988 | 0.00064771 | 0.0 | 0.00
Modify | 0.0046368 | 0.0047831 | 0.0050183 | 0.2 | 0.02
Other | | 0.01106 | | | 0.05
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 62390 ave 62390 max 62390 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 251260 ave 251260 max 251260 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1005040
Ave neighs/atom = 739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:21

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH.ILP Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/BNCH.ILP

1
examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.rebo Symbolic link
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@ -0,0 +1 @@
../../../../../potentials/CH.rebo

60
examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN
View File

@ -5,22 +5,23 @@ atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
group adsorbate type 3
group hBN molecule 1
group gr molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL NULL C # chemical
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N C # long range
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
@ -31,41 +32,26 @@ neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
fix thermostat all nve
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2
variable Ecoul equal c_3
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
# Calculate the pair potential between the substrate and slider
compute sldsub adsorbate group/group membrane
variable Evdw equal c_sldsub
############################
# Output
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify line one format float %.10f
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
run 1000

155
examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.1 Normal file
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@ -0,0 +1,155 @@
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000152684 secs
read_data CPU = 0.00139584 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
720 atoms in group hBN
group gr molecule 2
720 atoms in group gr
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify line one format float %.10f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10707.2836653377 -10763.0852699342 55.8016045965 -75.2477261362 -5401.7347845703 -5322.2780768034 -39.0724085605 36.1753175757 -75.2477261362 0.0000000000 300.0000000000
100 -10707.0738132278 -10737.1273434298 30.0535302020 -73.2173218622 -5389.9568321958 -5309.2004092412 -37.9701019928 35.2472198694 -73.2173218622 0.0000000000 161.5734731251
200 -10707.0160305531 -10734.9317906949 27.9157601418 -71.6030968581 -5389.1293717071 -5307.7455440517 -38.0568749361 33.5462219220 -71.6030968581 0.0000000000 150.0804162013
300 -10707.0133459577 -10734.9870508108 27.9737048532 -75.0821335395 -5388.9196081501 -5308.1164952096 -37.9509474511 37.1311860884 -75.0821335395 0.0000000000 150.3919379493
400 -10707.0118845924 -10735.4980560195 28.4861714271 -76.3398711857 -5389.1656629670 -5308.1529507210 -38.1794423315 38.1604288542 -76.3398711857 0.0000000000 153.1470553564
500 -10707.0073064907 -10734.6814074933 27.6741010026 -73.3123544614 -5388.7261058688 -5307.7383573628 -38.2169442617 35.0954101998 -73.3123544614 0.0000000000 148.7812108775
600 -10707.0179599067 -10735.8330915547 28.8151316481 -71.9277634955 -5389.0797599186 -5308.5959984739 -38.1573331622 33.7704303333 -71.9277634955 0.0000000000 154.9156078382
700 -10707.0202991119 -10735.6556762202 28.6353771083 -74.6793707186 -5389.2970704981 -5308.1866033124 -38.1720024097 36.5073683089 -74.6793707186 0.0000000000 153.9492133711
800 -10707.0042706783 -10734.3516957279 27.3474250495 -76.3712879764 -5388.5923210533 -5307.7206382682 -38.0387364064 38.3325515700 -76.3712879764 0.0000000000 147.0249390530
900 -10707.0144790011 -10735.8318835748 28.8174045738 -73.6993318112 -5388.9674133804 -5308.7963924816 -38.0680777128 35.6312540984 -73.6993318112 0.0000000000 154.9278275177
1000 -10706.9953891527 -10733.5615396283 26.5661504756 -71.4398677888 -5388.0186485439 -5307.4414386685 -38.1014524159 33.3384153730 -71.4398677888 0.0000000000 142.8246589021
Loop time of 55.1175 on 1 procs for 1000 steps with 1440 atoms
Performance: 1.568 ns/day, 15.310 hours/ns, 18.143 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 55.062 | 55.062 | 55.062 | 0.0 | 99.90
Bond | 0.00046717 | 0.00046717 | 0.00046717 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.034313 | 0.034313 | 0.034313 | 0.0 | 0.06
Output | 0.00034028 | 0.00034028 | 0.00034028 | 0.0 | 0.00
Modify | 0.010012 | 0.010012 | 0.010012 | 0.0 | 0.02
Other | | 0.01061 | | | 0.02
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8180 ave 8180 max 8180 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 140400 ave 140400 max 140400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 280800 ave 280800 max 280800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:55

155
examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.5Jun19.grhBN.icc.4 Normal file
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@ -0,0 +1,155 @@
LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000148868 secs
read_data CPU = 0.00332732 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
720 atoms in group hBN
group gr molecule 2
720 atoms in group gr
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify line one format float %.10f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10707.2836653376 -10763.0852699341 55.8016045965 -75.2477261361 -5401.7347845703 -5322.2780768034 -39.0724085604 36.1753175757 -75.2477261361 0.0000000000 300.0000000000
100 -10707.0738132277 -10737.1273434298 30.0535302020 -73.2173218622 -5389.9568321958 -5309.2004092412 -37.9701019928 35.2472198694 -73.2173218622 0.0000000000 161.5734731251
200 -10707.0160305531 -10734.9317906949 27.9157601418 -71.6030968581 -5389.1293717071 -5307.7455440517 -38.0568749361 33.5462219220 -71.6030968581 0.0000000000 150.0804162013
300 -10707.0133459576 -10734.9870508108 27.9737048532 -75.0821335395 -5388.9196081501 -5308.1164952096 -37.9509474511 37.1311860885 -75.0821335395 0.0000000000 150.3919379493
400 -10707.0118845923 -10735.4980560194 28.4861714271 -76.3398711857 -5389.1656629669 -5308.1529507210 -38.1794423315 38.1604288542 -76.3398711857 0.0000000000 153.1470553564
500 -10707.0073064907 -10734.6814074932 27.6741010026 -73.3123544614 -5388.7261058688 -5307.7383573628 -38.2169442616 35.0954101998 -73.3123544614 0.0000000000 148.7812108775
600 -10707.0179599066 -10735.8330915547 28.8151316481 -71.9277634955 -5389.0797599186 -5308.5959984739 -38.1573331622 33.7704303333 -71.9277634955 0.0000000000 154.9156078382
700 -10707.0202991119 -10735.6556762202 28.6353771083 -74.6793707186 -5389.2970704981 -5308.1866033124 -38.1720024097 36.5073683089 -74.6793707186 0.0000000000 153.9492133711
800 -10707.0042706783 -10734.3516957278 27.3474250495 -76.3712879764 -5388.5923210533 -5307.7206382682 -38.0387364063 38.3325515701 -76.3712879764 0.0000000000 147.0249390530
900 -10707.0144790010 -10735.8318835748 28.8174045738 -73.6993318112 -5388.9674133804 -5308.7963924816 -38.0680777128 35.6312540984 -73.6993318112 0.0000000000 154.9278275177
1000 -10706.9953891527 -10733.5615396283 26.5661504756 -71.4398677888 -5388.0186485439 -5307.4414386685 -38.1014524158 33.3384153730 -71.4398677888 0.0000000000 142.8246589021
Loop time of 15.7325 on 4 procs for 1000 steps with 1440 atoms
Performance: 5.492 ns/day, 4.370 hours/ns, 63.563 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.905 | 14.645 | 15.391 | 14.5 | 93.08
Bond | 0.00029796 | 0.00040495 | 0.00046212 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.3261 | 1.0722 | 1.8116 | 53.4 | 6.82
Output | 0.00028242 | 0.00030932 | 0.00037515 | 0.0 | 0.00
Modify | 0.0046079 | 0.0047365 | 0.0048651 | 0.2 | 0.03
Other | | 0.01031 | | | 0.07
Nlocal: 360 ave 380 max 340 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4716 ave 4736 max 4696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 35100 ave 37050 max 33150 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 70200 ave 74100 max 66300 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

1427
src/USER-MISC/pair_ilp_graphene_hbn.cpp
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File diff suppressed because it is too large Load Diff

8
src/USER-MISC/pair_ilp_graphene_hbn.h
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@ -21,6 +21,8 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN)
#define LMP_PAIR_ILP_GRAPHENE_HBN_H
#include "pair.h"
#include "my_page.h"
#include <cmath>
namespace LAMMPS_NS {
@ -34,9 +36,10 @@ class PairILPGrapheneHBN : public Pair {
void coeff(int, char **);
double init_one(int, int);
void init_style();
void ILP_neigh();
void calc_normal();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
void calc_FRep(int, int);
void calc_FvdW(int, int);
double single(int, int, int, int, double, double, double, double &);
protected:
@ -74,7 +77,6 @@ class PairILPGrapheneHBN : public Pair {
void read_file( char * );
void allocate();
void ILP_neigh();
/* ----Calculate the long-range cutoff term */
inline double calc_Tap(double r_ij, double Rcut) {

1441
src/USER-MISC/pair_kolmogorov_crespi_full.cpp
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File diff suppressed because it is too large Load Diff

8
src/USER-MISC/pair_kolmogorov_crespi_full.h
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@ -21,6 +21,8 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull)
#define LMP_PAIR_KolmogorovCrespi_FULL_H
#include "pair.h"
#include "my_page.h"
#include <cmath>
namespace LAMMPS_NS {
@ -34,9 +36,10 @@ class PairKolmogorovCrespiFull : public Pair {
void coeff(int, char **);
double init_one(int, int);
void init_style();
void KC_neigh();
void calc_normal();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
void calc_FRep(int, int);
void calc_FvdW(int, int);
double single(int, int, int, int, double, double, double, double &);
protected:
@ -75,7 +78,6 @@ class PairKolmogorovCrespiFull : public Pair {
void read_file( char * );
void allocate();
void KC_neigh();
/* ----Calculate the long-range cutoff term */